In this study, we propose a new open-source simulation platform that comprises computeraided design and computer-aided engineering tools for highly automated evaluation of electric field distribution and neural activation during Deep Brain Stimulation (DBS). It will be shown how a Volume Conductor Model (VCM) is constructed and examined using Pythoncontrolled algorithms for generation, discretization and adaptive mesh refinement of the computational domain, as well as for incorporation of heterogeneous and anisotropic properties of the tissue and allocation of neuron models. The utilization of the platform is facilitated by a collection of predefined input setups and quick visualization routines. The accuracy of a VCM, created and optimized by the platform, was estimated by comparison with a commercial software. The results demonstrate no significant deviation between the models in the electric potential distribution. A qualitative estimation of different physics for the VCM shows an agreement with previous computational studies. The proposed computational platform is suitable for an accurate estimation of electric fields during DBS in scientific modeling studies. In future, we intend to acquire SDA and EMA approval. Successful incorporation of open-source software, controlled by in-house developed algorithms, provides a highly automated solution. The platform allows for optimization and uncertainty quantification (UQ) studies, while employment of the open-source software facilitates accessibility and reproducibility of simulations.

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Background Electronic Laboratory Notebooks (ELNs) are used to document experiments and investigations in the wet-lab. Protocols in ELNs contain a detailed description of the conducted steps including the necessary information to understand the procedure and the raised research data as well as to reproduce the research investigation. The purpose of this study is to investigate whether such ELN protocols can be used to create semantic documentation of the provenance of research data by the use of ontologies and linked data methodologies. Methods Based on an ELN protocol of a biomedical wet-lab experiment, a retrospective provenance model of the raised research data describing the details of the experiment in a machine-interpretable way is manually engineered. Furthermore, an automated approach for knowledge acquisition from ELN protocols is derived from these results. This structure-based approach exploits the structure in the experiment’s description such as headings, tables, and links, to translate the ELN protocol into a semantic knowledge representation. To satisfy the Findable, Accessible, Interoperable, and Reuseable (FAIR) guiding principles, a ready-to-publish bundle is created that contains the research data together with their semantic documentation. Results While the manual modelling efforts serve as proof of concept by employing one protocol, the automated structure-based approach demonstrates the potential generalisation with seven ELN protocols. For each of those protocols, a ready-to-publish bundle is created and, by employing the SPARQL query language, it is illustrated that questions about the processes and the obtained research data can be answered. Conclusions The semantic documentation of research data obtained from the ELN protocols allows for the representation of the retrospective provenance of research data in a machine-interpretable way. Research Object Crate (RO-Crate) bundles including these models enable researchers to easily share the research data including the corresponding documentation, but also to search and relate the experiment to each other.

We present a model for exact recursive Bayesian filtering based on lifted multiset states. Combining multisets with lifting makes it possible to simultaneously exploit multiple strategies for reducing inference complexity when compared to list-based grounded state representations. The core idea is to borrow the concept of Maximally Parallel Multiset Rewriting Systems and to enhance it by concepts from Rao-Blackwellization and Lifted Inference, giving a representation of state distributions that enables efficient inference. In worlds where the random variables that define the system state are exchangeable -where the identity of entities does not matter -it automatically uses a representation that abstracts from ordering (achieving an exponential reduction in complexity) -and it automatically adapts when observations or system dynamics destroy exchangeability by breaking symmetry.

Tasks such as social network analysis, human behavior recognition, or modeling biochemical reactions, can be solved elegantly by using the probabilistic inference framework. However, standard probabilistic inference algorithms work at a propositional level, and thus cannot capture the symmetries and redundancies that are present in these tasks.Algorithms that exploit those symmetries have been devised in different research fields, for example by the lifted inference-, multiple object tracking-, and modeling and simulationcommunities. The common idea, that we call state space abstraction, is to perform inference over compact representations of sets of symmetric states. Although they are concerned with a similar topic, the relationship between these approaches has not been investigated systematically.This survey provides the following contributions. We perform a systematic literature review to outline the state of the art in probabilistic inference methods exploiting symmetries. From an initial set of more than 4,000 papers, we identify 116 relevant papers. Furthermore, we provide new high-level categories that classify the approaches, based on common properties of the approaches. The research areas underlying each of the categories are introduced concisely. Researchers from different fields that are confronted with a state space explosion problem in a probabilistic system can use this classification to identify possible solutions. Finally, based on this conceptualization, we identify potentials for future research, as some relevant application domains are not addressed by current approaches.

The reconstruction of human activities is an important prerequisite to provide assistance. In this paper, we present an activity and plan recognition approach which is based on causal models of human activities. We show, that it is possible to estimate current activities, the underlying goal of the user, and context information about the state of the environment from noisy sensor data. Therefore we use real world data obtained from a smart home system while observing unrestricted activities of daily living in an inhabited flat. We evaluate the accuracy of the recognition for simulated data of different granularity and data obtained from the smart home system. We furthermore show that performance measures solely based on action sequences are not sufficient to evaluate a recognition system.

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